rs8062326

Variant names:

• chr16-19144694-G-A
• rs8062326
• ENST00000564808.6:n.642+17409G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564808.6(ENSG00000261427):​n.642+17409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 152,258 control chromosomes in the GnomAD database, including 384 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.060 (384 hom., cov: 32)
• Consequence: ENSG00000261427 ENST00000564808.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 10 publications found

Genes affected

ENSG00000261427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564808.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261427	ENST00000564808.6	TSL:4	n.642+17409G>A		intron	N/A
	ENSG00000261427	ENST00000568526.1	TSL:5	n.212-8394G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0603 AC: 9173 AN: 152140 Hom.: 381 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0526

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0603 AC: 9179 AN: 152258 Hom.: 384 Cov.: 32 AF XY: 0.0620 AC XY: 4613 AN XY: 74442

African (AFR) AF: 0.104 AC: 4332 AN: 41534

American (AMR) AF: 0.0748 AC: 1144 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5178

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4826

European-Finnish (FIN) AF: 0.0848 AC: 899 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2367 AN: 68024

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0406 Hom.: 536

Bravo AF: 0.0615

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.68
PhyloP100		-0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8062326;

hg19: chr16-19156016;